SangerAlignment Level

SangerContig Level

SangerRead Level

Basic Information:

  • Output Directory : /Users/camilogarcia/Documents/Teaching/BiologyCourses/BI0487/Lectures/biocomp-book/chs-challenges-demos/data/sanger-processed/SangerAlignment/321_WT_
  • Input Source : ABIF
  • Process Method : REGEX
  • Input ABIF Directory : data/sanger-seqs/rpoB//.
  • Forward Reads Suffix Regex : rpoB_1_F.ab1
  • Reverse Reads Suffix Regex : rpoB_2_R.ab1
  • Contig Name : 321_WT_
  • Forward Read Number : 1
  • Reverse Read Number : 1

‘SangerContig’ Input Parameters :

  • Minimum Read Number : 2
  • Minimum Read Length : 20
  • Minimum Fraction Call : 0.5
  • Maximum Fraction Lost : 0.5
  • Accept Stop Codons : TRUE
  • Reading Frame : 1

Contig Sequence:

Primary Sequence

Reference Amino Sequence :

Genetic Code

Reference Amino Acid Sequence

‘refAminoAcidSeq’ is empty. There are no ‘refAminoAcidSeq’ in this SangerContig.

Contig Results:

Reads Alignment 

                                                    20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300                 320                 340                 360                 380                 400                 420                 440                 460                 480                 500                 520                 540                 560                 580                 600                 620                 640                 660                 680                 700                 720                 740                 760                 780                 800                 820                 840                 860                 880                 900                 920                 940                 960                 980                1000                1020                1040        
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    1_Read_321_WT_rpoB_1_F.ab1    ------------------------CGTCTTGTGA-GGATGATGTTTATACATCTATCCATATTGAAGAATATGAATCAGAAGCACGTGATACGAAACTTGGACCTGAAGAAATCACTCGCGATATTCCAAACGTCGGTGAAGATGCGCTTCGCAATCTTGATGACCGCGGAATCATCCGTATTGGGGCAGAAGTAAAAGACGGAGATCTTCTTGTTGGTAAAGTAACGCCTAAAGGTGTAACCGAACTGACTGCTGAAGAACGCCTTCTTCACGCCATCTTTGGTGAAAAAGCCCGCGAGGTTCGTGATACTTCTCTTCGTGTGCCTCACGGCGGCGGCGGAATTATCCACGACGTTAAAGTCTTCAACCGTGAAGACGGAGACGAACTTCCTCCAGGTGTAAACCAGTTGGTACGCGTATATATCGTTCAGAAACGTAAGATTTCTGAAGGGGATAAAATGGCCGGTCGTCACGGTAACAAAGGTGTTATCTCTAAGATTCTTCCTGAAGAGGATATGCCTTACCTTCCTGACGGCACACCAATTGACATCATGCTTAACCCGCTGGGCGTACCATCACGTATGAACATCGGGCAGGTATTGGAGCTTCATATGGGTATGGCCGCTCGTTACCTCGGCATTCACATTGCGTCTCCAGTATTTGATGGAGCGCGAGAAGAGGATGTTTGGGAAACACTTGAAGAAGCCGGCATGTCTCGTGACGCCAAA-CGGTGCTTTACGACGGACGTACTGGAGAGCCGTTTGATAACCGCGTGTCTGTCGGTATCATGTACATGATCAAACTGGCACACATGGTTGACGATAAACTTCATGCACGCTCTACAGGTCCTTACTCACTTGTTACGCAGCAGCCTCTTGGCGGTAAAGCGCAATTTGGCGGACAGCGTTT--GTGAGATGGTAGTTTGGGCACTTGAAGCTTATGGTGCAGCT-ACACTCTTCAAGAAATTCTGACTGTTA-GTCCGATAACTTGATTGGACGTGTGAAACTACATCTCTCTGGCACAAAAAAAAAAAAAAAAAAAAAAAAAAAA    1026    
    2_Read_321_WT_rpoB_2_R.ab1    TGAGGAGCCATCATCATGAGTGAACGTCTTGTGAAGGATGATGTTTATACATCTATCCATAT-GAAGAATATGAATCAGAAGCACGTGATACGAAACTTGGACCTGAAGAAATCACTCGCGATATTCCAAACGTCGGTGAAGATGCGCTTCGCAATCTTGATGACCGCGGAATCATCCGTATTGGGGCAGAAGTAAAAGACGGAGATCTTCTTGTTGGTAAAGTAACGCCTAAAGGTGTAACCGAACTGACTGCTGAAGAACGC-TTCTTCACGCCATCTTTGGTGAAAAAGCCCGCGAGGTTCGTGATACTTCTCTTCGTGTGCCTCACGGCGGCGGCGGAATTATCCACGACGTTAAAGTCTTCAACCGTGAAGACGGAGACGAACTTCCTCCAGGTGTAAACCAGTTGGTACGCGTATATATCGTTCAGAAACGTAAGATTTCTGAAGGGGATAAAATGGCCGGTCGTCACGGTAACAAAGGTGTTATCTCTAAGATTCTTCCTGAAGAGGATATGCCTTACCTTCCTGACGGCACACCAATTGACATCATGCTTAACCCGCTGGGCGTACCATCACGTATGAACATCGGGCAGGTATTGGAGCTTCATATGGGTATGGCCGCTCGTTACCTCGGCATTCACATTGCGTCTCCTGTATTTGATGGAGCGCGAGAAGAGGATGTTTGGGAAACACTTGAAGAAGCCGGCATGTCTCGTGACGCCAAAACGGTGCTTTACGACGGACGTACTGGAGAGCCGTTTGATAACCGCGTGTCTGTCGGTATCATGTACATGATCAAACTGGCACACATGGTTGACGATAAACTTCATGCACGCTCTACAGGTCCTTACTCACTTGTTACGCAGCAGCCTCTTGGCGGTAAAGCGCAATTTGGCGGACAGCGTTTTGGTGAGATGGAGGTTTGGGCACTTGAAGCTTATGGTGCAGCTTACACTCTTCAAGAAATTCTGACTGTTAAGTCCGAT------------------------------------------------------------------    988    
                     Consensus    TGAGGAGCCATCATCATGAGTGAACGTCTTGTGAAGGATGATGTTTATACATCTATCCATATTGAAGAATATGAATCAGAAGCACGTGATACGAAACTTGGACCTGAAGAAATCACTCGCGATATTCCAAACGTCGGTGAAGATGCGCTTCGCAATCTTGATGACCGCGGAATCATCCGTATTGGGGCAGAAGTAAAAGACGGAGATCTTCTTGTTGGTAAAGTAACGCCTAAAGGTGTAACCGAACTGACTGCTGAAGAACGCCTTCTTCACGCCATCTTTGGTGAAAAAGCCCGCGAGGTTCGTGATACTTCTCTTCGTGTGCCTCACGGCGGCGGCGGAATTATCCACGACGTTAAAGTCTTCAACCGTGAAGACGGAGACGAACTTCCTCCAGGTGTAAACCAGTTGGTACGCGTATATATCGTTCAGAAACGTAAGATTTCTGAAGGGGATAAAATGGCCGGTCGTCACGGTAACAAAGGTGTTATCTCTAAGATTCTTCCTGAAGAGGATATGCCTTACCTTCCTGACGGCACACCAATTGACATCATGCTTAACCCGCTGGGCGTACCATCACGTATGAACATCGGGCAGGTATTGGAGCTTCATATGGGTATGGCCGCTCGTTACCTCGGCATTCACATTGCGTCTCCWGTATTTGATGGAGCGCGAGAAGAGGATGTTTGGGAAACACTTGAAGAAGCCGGCATGTCTCGTGACGCCAAAACGGTGCTTTACGACGGACGTACTGGAGAGCCGTTTGATAACCGCGTGTCTGTCGGTATCATGTACATGATCAAACTGGCACACATGGTTGACGATAAACTTCATGCACGCTCTACAGGTCCTTACTCACTTGTTACGCAGCAGCCTCTTGGCGGTAAAGCGCAATTTGGCGGACAGCGTTTTGGTGAGATGGWRGTTTGGGCACTTGAAGCTTATGGTGCAGCTTACACTCTTCAAGAAATTCTGACTGTTAAGTCCGATAACTTGATTGGACGTGTGAAACTACATCTCTCTGGCACAAAAAAAAAAAAAAAAAAAAAAAAAAAA    1056    
                                          
                     Consensus    TGAGGAGCCATCATCATGAGTGAACGTCTTGTGA+GGATGATGTTTATACATCTATCCATAT+GAAGAATATGAATCAGAAGCACGTGATACGAAACTTGGACCTGAAGAAATCACTCGCGATATTCCAAACGTCGGTGAAGATGCGCTTCGCAATCTTGATGACCGCGGAATCATCCGTATTGGGGCAGAAGTAAAAGACGGAGATCTTCTTGTTGGTAAAGTAACGCCTAAAGGTGTAACCGAACTGACTGCTGAAGAACGC+TTCTTCACGCCATCTTTGGTGAAAAAGCCCGCGAGGTTCGTGATACTTCTCTTCGTGTGCCTCACGGCGGCGGCGGAATTATCCACGACGTTAAAGTCTTCAACCGTGAAGACGGAGACGAACTTCCTCCAGGTGTAAACCAGTTGGTACGCGTATATATCGTTCAGAAACGTAAGATTTCTGAAGGGGATAAAATGGCCGGTCGTCACGGTAACAAAGGTGTTATCTCTAAGATTCTTCCTGAAGAGGATATGCCTTACCTTCCTGACGGCACACCAATTGACATCATGCTTAACCCGCTGGGCGTACCATCACGTATGAACATCGGGCAGGTATTGGAGCTTCATATGGGTATGGCCGCTCGTTACCTCGGCATTCACATTGCGTCTCCWGTATTTGATGGAGCGCGAGAAGAGGATGTTTGGGAAACACTTGAAGAAGCCGGCATGTCTCGTGACGCCAAA+CGGTGCTTTACGACGGACGTACTGGAGAGCCGTTTGATAACCGCGTGTCTGTCGGTATCATGTACATGATCAAACTGGCACACATGGTTGACGATAAACTTCATGCACGCTCTACAGGTCCTTACTCACTTGTTACGCAGCAGCCTCTTGGCGGTAAAGCGCAATTTGGCGGACAGCGTTT++GTGAGATGGWRGTTTGGGCACTTGAAGCTTATGGTGCAGCT+ACACTCTTCAAGAAATTCTGACTGTTA+GTCCGATAACTTGATTGGACGTGTGAAACTACATCTCTCTGGCACAAAAAAAAAAAAAAAAAAAAAAAAAAAA    1056

Difference Data Frame

name pairwise.diffs.to.consensus unused.chars
1_Read_321_WT_rpoB_1_F.ab1 3 0
2_Read_321_WT_rpoB_2_R.ab1 3 0

Distance Matrix

1_Read_321_WT_rpoB_1_F.ab1 2_Read_321_WT_rpoB_2_R.ab1
1_Read_321_WT_rpoB_1_F.ab1 0.0000000 0.0031381
2_Read_321_WT_rpoB_2_R.ab1 0.0031381 0.0000000

Dendrogram

cluster
1_Read_321_WT_rpoB_1_F.ab1 2
2_Read_321_WT_rpoB_2_R.ab1 1

Indels Data Frame

‘indelsDF’ Data Frame is empty.


Stop Codons

‘stopCodonsDF’ Data Frame is empty.


Secondary Peak Data Frame

‘secondaryPeakDF’ Data Frame is empty.



Forward Read Reports

Reverse Read Reports




Back to ‘SangerAlignment Report’